This study evaluates the anthocyanin and derived pigment composition of Vitis vinifera red wines of Vranec, Merlot, and Cabernet Sauvignon produced in 2006 vintages from the Tikveš wine region in the Republic of Macedonia. Their profile was established using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) technique. A total of 22 anthocyanins and derived pigments have been identified in the samples including 10 anthocyanins, 1 ethyl-bridged flavanol-anthocyanin adduct, and 11 pyranoanthocyanins. MALDI-TOF-MS analysis was performed after solid-phase extraction of the wines by using, for the first time, the Zip-Tip® C18 stationary phase, introducing a novel small-scale sample cleanup procedure prior to the rapid MALDI-TOF-MS fingerprinting of wine samples. 2′,4′,6′-Trihydroxyacetophenone (dissolved in acetonitrile/water 1:1, v/v) was used as a matrix. The qualitative screening of anthocyanins and derived pigments with MALDI-TOF-MS confirmed the presence of glucoside, acetylglucoside, and p-coumaroylglucoside derivatives of anthocyanins in the wine samples. Furthermore, pyranoanthocyanins formed by reactions of anthocyanins with pyruvic acid and acetaldehyde, as well as flavanol-pyranoanthocyanins and ethyl-bridged flavan-3-ol-anthocyanin adduct pigments have been detected in the samples.